The Kim Scott Walwyn prize, set up in 2004 to celebrate outstanding achievements by women in publishing, has been awarded to the head of the Nature Publishing Group, Annette Thomas.

Thomas beat Rebecca Carter, editor-at-large at Random House, and Oxford University Press's head of marketing, Susanna Lob, to take the £3,000 prize. It honours a career that includes 14 years at Nature Publishing Group, where Thomas rose from the role of assistant editor to her current position as managing director, and her appointment in 2000 to an executive director's position at Macmillan Publishers.

The prizegiving took place yesterday evening at St Anne's College, Oxford. The prize committee was chaired by Dame Gillian Beer, professor emeritus at Cambridge University, and included the literary agent Catherine Clarke and the writer Hermione Lee. Speaking after the award, Dame Gillian praised Thomas's achievement. "Annette's 14-year career with the group has been remarkable," she said, "acted out in the very competitive, fast-moving and intellectually demanding world of international science and medical research."

The prize, which is administered by the independent reading charity Booktrust, commemorates the life and career of Kim Scott Walwyn, a pioneering publishing director at OUP, who died in 2002, aged just 45. It was conceived by Catherine Clarke and Hermione Lee, both friends of Walwyn. In the words of Lee, they "wanted her short life to have an afterlife".

"Publishing is one of the industries in which women have been able to forge careers that takes them to the top, but I still think it hides a lot of very talented women who are achieving huge things," said Clarke, explaining the need for the prize. "This reflects Kim herself: she was great at bringing out other people but didn't put herself forward. It is wonderful to be able to honour women whose work would not otherwise receive public recognition."

Previous winners of the prize were Lynette Owen, copyright director of Pearson Education, and Penelope Hoare, deputy publishing director of Chatto and Windus.